Interoperability is a multifaceted problem caused by issues surpassing those of technological incompatibilities. The real interoperability challenges are stemming from various sources, such as organisational incompatibilities buried deeply into the structures of collaborating enterprises, architectural mismatches and defective assumptions about business application behaviour, or from the inherent properties of business collaboration models. To achieve interoperability in enterprise computing environments, the aspects of interoperability must be identied and their properties analysed. This paper studies interoperability issues in enterprise computing environments. Enterprise computing environments under analysis are based on Service Oriented Computing paradigm and enhanced with necessary infrastructure facilities. Several classes of causes for interoperability problems are identied and the mechanisms for overcoming the problems in these classes are briey discussed.